Apical fenestration is a defect in the alveolar cortical plate, exposing the root without involving the alveolar bone margin, often linked to trauma, periodontal disease, and orthodontic treatment, leading to symptoms such as pain and abscesses from endodontic infections. This case report describes managing a mucosal fenestration in an endodontically treated tooth with nonsurgical root canal therapy and periodontal surgery. A 44-year-old male presented with mucosal fenestration and pain in the upper front jaw due to trauma and an inadequately treated root canal. Examination revealed an ill-fitting crown and an open apex with periapical radiolucency. Treatment included scaling, root planing, nonsurgical root canal therapy, apexification using Biodentine, and obturation with bioceramic sealer. Persistent fenestration necessitated periodontal surgery to remove extruded material and place an alloplastic graft. Apical fenestrations, although uncommon, require coordinated endodontic and periodontal treatment for successful outcomes.